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- PDB-1pp9: Bovine cytochrome bc1 complex with stigmatellin bound -

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Basic information

Entry
Database: PDB / ID: 1pp9
TitleBovine cytochrome bc1 complex with stigmatellin bound
Components
  • (Ubiquinol-cytochrome C reductase complex ...) x 6
  • (Ubiquinol-cytochrome C reductase iron-sulfur subunit, ...) x 2
  • Cytochrome b
  • Cytochrome c1, heme protein, mitochondrial
KeywordsOXIDOREDUCTASE / CYTOCHROME BC1 / MEMBRANE PROTEIN / HEME PROTEIN / RIESKE IRON SULFUR PROTEIN / CYTOCHROME B / CYTOCHROME C1 / COMPLEX III / MITOCHONDRIAL PROCESSING PROTEASE / MPP UBIQUINONE / REDOX ENZYME / RESPIRATORY CHAIN / STIGMATELLIN
Function / homology
Function and homology information


mitochondrial respiratory chain complex III assembly / Respiratory electron transport / mitochondrial respiratory chain complex III / mitochondrial respiratory chain complex IV / quinol-cytochrome-c reductase / ubiquinone binding / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / respiratory electron transport chain ...mitochondrial respiratory chain complex III assembly / Respiratory electron transport / mitochondrial respiratory chain complex III / mitochondrial respiratory chain complex IV / quinol-cytochrome-c reductase / ubiquinone binding / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / respiratory electron transport chain / mitochondrial membrane / 2 iron, 2 sulfur cluster binding / metalloendopeptidase activity / mitochondrial inner membrane / oxidoreductase activity / heme binding / mitochondrion / proteolysis / membrane / metal ion binding
Similarity search - Function
Cytochrome Bc1 Complex; Chain I / Cytochrome Bc1 Complex; Chain I / Ubiquinol cytochrome reductase, transmembrane domain / Cytochrome Bc1 Complex; Chain F / Cytochrome b-c1 complex subunit 7 / Ubiquinol-cytochrome C reductase hinge domain / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 9 / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C ...Cytochrome Bc1 Complex; Chain I / Cytochrome Bc1 Complex; Chain I / Ubiquinol cytochrome reductase, transmembrane domain / Cytochrome Bc1 Complex; Chain F / Cytochrome b-c1 complex subunit 7 / Ubiquinol-cytochrome C reductase hinge domain / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 9 / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Cytochrome c1, transmembrane anchor, C-terminal / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / Globular protein, non-globular alpha/beta subunit / Cytochrome b-c1 complex, subunit 6 / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome c1, transmembrane anchor, C-terminal / 3-layer Sandwich / Cytochrome b / : / : / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome c1 / Cytochrome C1 family / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Ribbon / Helix Hairpins / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
AZIDE ION / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / hexyl beta-D-glucopyranoside / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / PHOSPHATE ION / STIGMATELLIN A / Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer ...AZIDE ION / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / hexyl beta-D-glucopyranoside / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / PHOSPHATE ION / STIGMATELLIN A / Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer / Cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 6, mitochondrial / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 9 / Cytochrome b / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b-c1 complex subunit 2, mitochondrial / Cytochrome b-c1 complex subunit 1, mitochondrial
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT USING NATIVE BOVINE, STIGMATELLIN-BOUND CHICKEN STRUCTURES / Resolution: 2.1 Å
AuthorsHuang, L.S. / Cobessi, D. / Tung, E.Y. / Berry, E.A.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Binding of the Respiratory Chain Inhibitor Antimycin to the Mitochondrial bc(1) Complex: A New Crystal Structure Reveals an Altered Intramolecular Hydrogen-bonding Pattern.
Authors: Huang, L.S. / Cobessi, D. / Tung, E.Y. / Berry, E.A.
History
DepositionJun 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 29, 2014Group: Non-polymer description
Revision 1.4Oct 11, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Revision 2.0Dec 20, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / entity ...atom_site / entity / pdbx_distant_solvent_atoms / struct_site
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _struct_site.details
Revision 2.1Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / pdbx_struct_conn_angle ...chem_comp / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Aug 16, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquinol-cytochrome C reductase complex core protein I, mitochondrial
B: Ubiquinol-cytochrome C reductase complex core protein 2, mitochondrial
C: Cytochrome b
D: Cytochrome c1, heme protein, mitochondrial
E: Ubiquinol-cytochrome C reductase iron-sulfur subunit, mitochondrial
F: Ubiquinol-cytochrome C reductase complex 14 kDa protein
G: Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein QP-C
H: Ubiquinol-cytochrome C reductase complex 11 kDa protein
I: Ubiquinol-cytochrome C reductase iron-sulfur subunit, mitochondrial
J: Ubiquinol-cytochrome C reductase complex 7.2 kDa protein
N: Ubiquinol-cytochrome C reductase complex core protein I, mitochondrial
O: Ubiquinol-cytochrome C reductase complex core protein 2, mitochondrial
P: Cytochrome b
Q: Cytochrome c1, heme protein, mitochondrial
R: Ubiquinol-cytochrome C reductase iron-sulfur subunit, mitochondrial
S: Ubiquinol-cytochrome C reductase complex 14 kDa protein
T: Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein QP-C
U: Ubiquinol-cytochrome C reductase complex 11 kDa protein
V: Ubiquinol-cytochrome C reductase iron-sulfur subunit, mitochondrial
W: Ubiquinol-cytochrome C reductase complex 7.2 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)491,20761
Polymers469,53220
Non-polymers21,67541
Water25,8881437
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area111270 Å2
ΔGint-775 kcal/mol
Surface area146660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.117, 171.055, 227.204
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.672875, 0.240986, 0.699404), (0.240986, -0.822471, 0.515235), (0.699404, 0.515235, 0.495346)
Vector: 11.98966, 106.87673, -42.43319)

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Components

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Ubiquinol-cytochrome C reductase complex ... , 6 types, 12 molecules ANBOFSGTHUJW

#1: Protein Ubiquinol-cytochrome C reductase complex core protein I, mitochondrial / CYTOCHROME BC1 COMPLEX / COMPLEX III


Mass: 49266.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P31800, quinol-cytochrome-c reductase
#2: Protein Ubiquinol-cytochrome C reductase complex core protein 2, mitochondrial / Complex III subunit II


Mass: 46575.469 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P23004, quinol-cytochrome-c reductase
#6: Protein Ubiquinol-cytochrome C reductase complex 14 kDa protein / Complex III subunit VI


Mass: 13371.190 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00129, quinol-cytochrome-c reductase
#7: Protein Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein QP-C / Ubiquinol-cytochrome C reductase complex 9.5 kDa protein / Complex III subunit VII


Mass: 9606.027 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13271, quinol-cytochrome-c reductase
#8: Protein Ubiquinol-cytochrome C reductase complex 11 kDa protein / Mitochondrial hinge protein / Cytochrome C1 / nonheme 11 kDa protein / Complex III subunit VIII


Mass: 9189.116 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00126, quinol-cytochrome-c reductase
#10: Protein Ubiquinol-cytochrome C reductase complex 7.2 kDa protein / Cytochrome C1 / nonheme 7 kDa protein / Complex III subunit X


Mass: 7209.311 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00130, quinol-cytochrome-c reductase

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Protein , 2 types, 4 molecules CPDQ

#3: Protein Cytochrome b / / CYTOCHROME BC1 COMPLEX / COMPLEX III


Mass: 42620.340 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00157, quinol-cytochrome-c reductase
#4: Protein Cytochrome c1, heme protein, mitochondrial / / Cytochrome c-1


Mass: 27323.277 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00125, quinol-cytochrome-c reductase

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Ubiquinol-cytochrome C reductase iron-sulfur subunit, ... , 2 types, 4 molecules ERIV

#5: Protein Ubiquinol-cytochrome C reductase iron-sulfur subunit, mitochondrial / Rieske iron-sulfur protein / RISP / Complex III subunit IX


Mass: 21640.580 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13272, quinol-cytochrome-c reductase
#9: Protein Ubiquinol-cytochrome C reductase iron-sulfur subunit, mitochondrial / Rieske iron-sulfur protein / RISP / Complex III subunit IX


Mass: 7964.259 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13272, quinol-cytochrome-c reductase

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Sugars , 1 types, 6 molecules

#11: Sugar
ChemComp-JZR / hexyl beta-D-glucopyranoside / hexyl beta-D-glucoside / hexyl D-glucoside / hexyl glucoside


Type: D-saccharide / Mass: 264.315 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H24O6

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Non-polymers , 11 types, 1472 molecules

#12: Chemical
ChemComp-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: N3
#13: Chemical
ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE / Discrete optimized protein energy


Mass: 744.034 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C41H78NO8P / Comment: DOPE, phospholipid*YM
#14: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#15: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#16: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#17: Chemical ChemComp-SMA / STIGMATELLIN A


Mass: 514.650 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H42O7
#18: Chemical ChemComp-UQ / Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer


Mass: 863.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C59H90O4
#19: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#20: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#21: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL / Cardiolipin


Mass: 1464.043 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#22: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1437 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.883 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 277 K / pH: 6.65
Details: PEG-3350, JEFFAMINE, GLYCEROL, CACODYLATE, HEXYLGLUCOSIDE, pH 6.65, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.992
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 28, 2002
Details: SI(311)MONOCHROMATOR (HORIZONTAL) FLAT MIRROR (VERTICAL)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.992 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 312369 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 27.3 Å2 / Rsym value: 0.12 / Net I/σ(I): 10.9
Reflection shellResolution: 2.1→2.18 Å / Mean I/σ(I) obs: 1.037 / Rsym value: 0.99 / % possible all: 83

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
TRUNCATEmodel building
AMoRE(CCP4 PACKAGE)phasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT USING NATIVE BOVINE, STIGMATELLIN-BOUND CHICKEN STRUCTURES
Starting model: PDB ENTRIES 1BE3, 2BCC

1be3

2bcc


Resolution: 2.1→24.98 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 6574455.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: A NUMBER OF DIFFERENT DATASETS WERE USED IN THE STRUCTURE DETERMINATION IN ADDITION TO THE DATASET USED FOR THE FINAL REFINEMENT PRESENTED HERE. THE ORIGINAL MOLECULAR REPLACEMENT WAS ...Details: A NUMBER OF DIFFERENT DATASETS WERE USED IN THE STRUCTURE DETERMINATION IN ADDITION TO THE DATASET USED FOR THE FINAL REFINEMENT PRESENTED HERE. THE ORIGINAL MOLECULAR REPLACEMENT WAS CARRIED OUT WITH A LOWER RESOLUTION DATASET. DUE TO LARGE VARIATIONS IN THE CELL PARAMETERS, EACH NEW DATASET WAS RE-SOLVED BY MOLECULAR REPLACEMENT USING A PREVIOUS MODEL. THE SAME R-FREE SET WAS USED IN ALL CASES. STRONG NCS RESTRAINTS WERE USED IN POSITIONAL REFINEMENT. THE COMPLEX WAS DIVIDED INTO 49 TWO-FOLD NCS GROUPS. SPECIFIC RESIDUES NOT OBEYING NCS WERE IDENTIFIED AND RELEASED FROM THE CONSTRAINT. NO NCS RESTRAINT ON B-FACTOR WAS USED. AFTER REFINEMENT TO CONVERGENCE AGAINST THE WORKING SET OF REFLECTIONS, THE R- AND R-FREE VALUES OF 0.250 AND 0.287 WERE OBTAINED. A FINAL ROUND OF POSITIONAL MINIMIZATION AND RESTRAINED B-FACTOR REFINEMENT WAS CARRIED OUT WITH IDENTICAL PARAMETERS BUT AGAINST ALL THE DATA, GIVING AN R-FACTOR OF 0.2609. THE SUBMITTED COORDINATES ARE FROM THIS FINAL NON-CV REFINEMENT.RESIDUE (GLU 12 ) AND RESIDUE (VAL 17 ) ARE LINKED TOGETHER FOR CHAIN B AND O. SEQUENCE ASSIGNMENT FOR THIS FRAGMENT IS AMBIGUOUS.
RfactorNum. reflection% reflectionSelection details
Rfree0.287 15194 5 %RANDOM
Rwork0.25 ---
obs0.25 305496 97.3 %-
all-305496 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.6 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso mean: 46.9 Å2
Baniso -1Baniso -2Baniso -3
1-15.35 Å20 Å20 Å2
2---0.55 Å20 Å2
3----14.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.1→24.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31493 0 1029 1437 33959
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it2.212
X-RAY DIFFRACTIONc_scbond_it2.152
X-RAY DIFFRACTIONc_scangle_it3.392.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.1→2.15 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.402 889 4.7 %
Rwork0.397 18177 -
obs--91.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMCNS_TOPPAR:PROTEIN_NOHYDROGEN.TOP
X-RAY DIFFRACTION2WATER.PARAMCNS_TOPPAR:WATER.TOP
X-RAY DIFFRACTION3HETERO10.PARHETERO10.TOP
X-RAY DIFFRACTION4PROSTH4.PARPROSTH4.TOP

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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